Inferring ancestral amino acid composition

We have developed a method based on expectation-maximization for
estimating ancestral amino acid composition. On simulated data, the
approach was found to be very effective in estimating ancestral amino
acid composition, with accuracy improving as the number of residues in
the dataset was increased. We have also applied this method to infer
the amino acid composition of a set of proteins in the Last Universal
Ancestor of life.
Here is the source code and README for our software.

If you use this program in your research, please cite:

Dawn Brooks, Jacques Fresco and Mona Singh.
"A novel method for
estimating ancestral amino acid composition and its application to
proteins of the Last Universal Ancestor,"
Bionformatics, in press. Bioinformatics advance access
published on April 8, 2004. [Publisher's
site]